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Detailed information for vg0403670419:

Variant ID: vg0403670419 (JBrowse)	Variation Type: SNP
Chromosome: chr04	Position: 3670419
Reference Allele: C	Alternative Allele: G
Primary Allele: C	Secondary Allele: G

Inferred Ancestral Allele : C (evidence from allele frequency in Oryza rufipogon: C: 0.95, G: 0.05, others allele: 0.00, population size: 74. )

Flanking Sequence (100 bp) in Reference Genome:

CCAGCATCAGGCGAGGCCACACACGCTCCTCGTGCACGACCAGCCCGCAGAGCGCGTCCTGGCACGGCGCGTTCTGCACCGCCTCTGTCACAGCGAGCAA[C/G]
AAAGCTGGGCCAGCATCCTCAGTTTGCGCAAGATGAGCTTCAGCCTTCTTCTTCTTGGGGTGTGGACACTGCGTGGAGTAGTGGCCAAACTCCTCACAGT

Reverse complement sequence

ACTGTGAGGAGTTTGGCCACTACTCCACGCAGTGTCCACACCCCAAGAAGAAGAAGGCTGAAGCTCATCTTGCGCAAACTGAGGATGCTGGCCCAGCTTT[G/C]
TTGCTCGCTGTGACAGAGGCGGTGCAGAACGCGCCGTGCCAGGACGCGCTCTGCGGGCTGGTCGTGCACGAGGAGCGTGTGTGGCCTCGCCTGATGCTGG

Allele Frequencies:

Populations	Population Size	Frequency of C(primary allele)	Frequency of G(secondary allele)	Frequency of N	Frequency of DEL	Frequency of others Allele
All	4726	54.60%	24.70%	1.23%	19.47%	NA
All Indica	2759	62.70%	30.80%	1.38%	5.07%	NA
All Japonica	1512	43.60%	6.80%	0.73%	48.88%	NA
Aus	269	50.60%	40.90%	1.86%	6.69%	NA
Indica I	595	95.10%	4.20%	0.17%	0.50%	NA
Indica II	465	68.00%	28.00%	0.65%	3.44%	NA
Indica III	913	40.60%	49.20%	2.74%	7.45%	NA
Indica Intermediate	786	60.80%	31.30%	1.15%	6.74%	NA
Temperate Japonica	767	50.10%	0.30%	0.26%	49.41%	NA
Tropical Japonica	504	24.20%	18.10%	1.39%	56.35%	NA
Japonica Intermediate	241	63.50%	4.10%	0.83%	31.54%	NA
VI/Aromatic	96	10.40%	80.20%	1.04%	8.33%	NA
Intermediate	90	51.10%	28.90%	3.33%	16.67%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg0403670419	C -> DEL	LOC_Os04g06960.1	N	frameshift_variant	Average:28.192; most accessible tissue: Zhenshan97 flag leaf, score: 66.824	N	N	N	N
vg0403670419	C -> G	LOC_Os04g06960.1	missense_variant ; p.Leu130Phe; MODERATE	nonsynonymous_codon ; L130F	Average:28.192; most accessible tissue: Zhenshan97 flag leaf, score: 66.824	unknown	unknown	DELETERIOUS	0.01

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0403670419	3.27E-07	5.78E-08	mr1227	Jap_All	YES	Genome-wide association analyses provide genetic and biochemical insights into natural variation in rice metabolism, Nat Genet, 46(7):714-21, PMID:24908251
vg0403670419	NA	7.72E-09	mr1570	All	Not	Genome-wide association analyses provide genetic and biochemical insights into natural variation in rice metabolism, Nat Genet, 46(7):714-21, PMID:24908251
vg0403670419	NA	4.40E-06	mr1540_2	Ind_All	Not	Genome-wide association analyses provide genetic and biochemical insights into natural variation in rice metabolism, Nat Genet, 46(7):714-21, PMID:24908251
vg0403670419	NA	2.71E-07	mr1558_2	Ind_All	YES	Genome-wide association analyses provide genetic and biochemical insights into natural variation in rice metabolism, Nat Genet, 46(7):714-21, PMID:24908251